I understand they removed the Engineer vs Wayland and entourage scene for "mystery" and general "what-the-ef-ness", but the cut out scene makes so much more sense, we get to see why Engineer got angry and why he tore David to pieces like a little toy. Instead, after cutting it, Engineer was made to look like a psycho killer. Woke up, saw aliens in the bedroom, heard his language spoken by them and launched into range and fury chasing everyone across the set Friday 13th style. Facepalming omission that scene.
Also, Vickers' convo with daddy. So much better in cut out scene than in original you begin to wonder if Scott was still behind steering wheel in editing room. The cut out prologue is also better, takes away the questions - was proto-Engineer alone, was he banished, was it suicide, etc.